Mutation of a bHLH transcription factor allowed almond domestication

Sánchez‐Pérez, Raquel; Pavan, Stefano; Mazzeo, Rosa; MOLDOVAN, Claudiu; Cigliano, Riccardo Aiese; Cueto, Jorge Del; Ricciardi, Francesca; Lotti, Concetta; Ricciardi, Luigi M.; Dicenta, F.; López‐Marqués, Rosa L.; Møller, Birger Lindberg

doi:10.1126/science.aav8197

Cited by 135 publications

(123 citation statements)

References 78 publications

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“…The group of SNPs identified in the present study could prove useful for various marker-based applications in Prunus. In fact, the genus Prunus is well enabled with the availability of several reference genome sequences 25,26,[46][47][48][49] . However, it must be noted that each genome is prone to harbor insertions and deletions with respect to genomes from other species.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide SNP identification in Prunus rootstocks germplasm collections using Genotyping-by-Sequencing: phylogenetic analysis, distribution of SNPs and prediction of their effect on gene function

Guajardo

Solís

Almada

et al. 2020

Sci Rep

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Genotyping-by-Sequencing (GBS) was applied in a set of 53 diploid Prunus rootstocks and five scion cultivars from three subgenera (Amygdalus, Prunus and Cerasus) for genome-wide SNP identification and to assess genetic diversity of both Chilean and Spanish germplasm collections. A group of 45,382 high quality SNPs (MAF >0.05; missing data <5%) were selected for analysis of this group of 58 accessions. These SNPs were distributed in genic and intergenic regions in the eight pseudomolecules of the peach genome (Peach v2.0), with an average of 53% located in exonic regions. The genetic diversity detected among the studied accessions divided them in three groups, which are in agreement with their current taxonomic classification. SNPs were classified based on their putative effect on annotated genes and KOG analysis was carried out to provide a deeper understanding of the function of 119 genes affected by high-impact SNPs. Results demonstrate the high utility for Prunus rootstocks identification and studies of diversity in Prunus species. Also, given the high number of SNPs identified in exonic regions, this strategy represents an important tool for finding candidate genes underlying traits of interest and potential functional markers for use in marker-assisted selection.

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Section: Discussionmentioning

confidence: 99%

Genome-wide SNP identification in Prunus rootstocks germplasm collections using Genotyping-by-Sequencing: phylogenetic analysis, distribution of SNPs and prediction of their effect on gene function

Guajardo

Solís

Almada

et al. 2020

Sci Rep

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“…The recent introduction of long-read sequencing technologies and long-range scaffolding methods has enabled chromosome-scale assembly for multiple plant species, including highly heterozygous tree crops such as almond ( Prunus dulcis ; (Sánchez-Pérez et al 2019) and kiwifruit ( Actinidia eriantha ; (Tang et al 2019). The availability of genomes with fully assembled chromosomes provides foundations for understanding plant domestication and evolution (Jarvis et al 2017; Maccaferri et al 2019; Sánchez-Pérez et al 2019), the mechanisms governing important traits (e.g. flower color and scent; (Raymond et al 2018), as well as the impact of epigenetic modifications on phenotypic variability (Daccord et al 2017).…”

Section: Introductionmentioning

confidence: 99%

High-quality chromosome-scale assembly of the walnut (Juglans regiaL) reference genome

Marrano

Britton

Zaini

et al. 2019

Preprint

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27The release of the first reference genome of walnut (Juglans regia L.) enabled many achievements 28 in the characterization of walnut genetic and functional variation. However, it is highly 29 fragmented, preventing the integration of genetic, transcriptomic, and proteomic information to 30 fully elucidate walnut biological processes. Here we report the new chromosome-scale assembly 31 of the walnut reference genome (Chandler v2.0) obtained by combining Oxford Nanopore long-32 read sequencing with chromosome conformation capture (Hi-C) technology. Relative to the 33 previous reference genome, the new assembly features an 84.4-fold increase in N50 size, and the 34 full sequence of all 16 chromosomal pseudomolecules, nine of which present telomere sequences 35 at both ends. Using full-length transcripts from single-molecule real-time sequencing, we predicted 36 40,491 gene models, with a mean gene length higher than the previous gene annotations. Most of 37 the new protein-coding genes (90%) are full-length, which represents a significant improvement 38 compared to Chandler v1.0 (only 48%). We then tested the potential impact of the new 39 chromosome-level genome on different areas of walnut research. By studying the proteome 40 changes occurring during catkin development, we observed that the virtual proteome obtained 41 from Chandler v2.0 presents fewer artifacts than the previous reference genome, enabling the 42 identification of a new potential pollen allergen in walnut. Also, the new chromosome-scale 43 genome facilitates in-depth studies of intraspecies genetic diversity by revealing previously 44 undetected autozygous regions in Chandler, likely resulting from inbreeding, and 195 genomic 45 regions highly differentiated between Western and Eastern walnut cultivars. Overall, Chandler 46 v2.0 is a valuable resource to understand and explore walnut biology better.47 48Persian walnut (Juglans regia L.) is among the top three most-consumed nuts in the world, and 50 over the last ten years, its global production increased by 37% (International Nut and Dried Fruit 51

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“…Recently, more and more researches reveal that bHLH gene play important role in fruit development process, including tomato [11], peach [19], apple [20], almond [33] and Chinese jujube [34]. In this study, 91 HrbHLH mRNAs had an RPKM value greater than 1 in three fruit development stages.…”

Section: Discussionmentioning

confidence: 63%

“…The expression HrbHLH90 was signi cantly higher at the early stage of fruit development. This result also indicated that it might be involved in fruit enlargement [26,33]. In addition, the expression of HrbHLH91 and HrbHLH92 were signi cantly higher at the ripen stage of fruit development.…”

Section: Discussionmentioning

confidence: 68%

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Genome-Wide Analysis of Basic Helix-Loop-Helix (bHLH) TFs in Sea Buckthorn (Hippophae rhamnoides)

et al. 2020

Preprint

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Background The basic helix-loop-helix (bHLH) transcription factor gene family is one of the largest gene families and extensively involved in plant growth, organ development, and stress responses. However, limited studies are available on the gene family in sea buckthorn. Results In this study, we focused on 144 HrbHLH genes, exploring their DNA and protein sequences and physicochemical properties. According to their protein sequence similarities, we classified the genes into 15 groups with specific motif structures. In order to explore their expressions, we performed gene expression profiling using RNA-Seq and identified 108 HrbHLH genes that expressed in five sea buckthorn tissue, including root nodule, root, leaf, stem and fruit. Furthermore, we found 11 increased expressed HrbHLH genes during sea buckthorn fruit development. We validated the expression pattern of HrbHLH genes using reverse transcription quantitative real-time PCR. Conclusions This study lays the foundation for future studies on gene cloning, transgenes, and biological mechanisms. We performed a genome-wide, systematic analysis of bHLH proteins in sea buckthorn. This comprehensive analysis provides a useful resource that enables further investigation of the physiological roles and molecular functions of the HrbHLH TFs.

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Mutation of a bHLH transcription factor allowed almond domestication

Cited by 135 publications

References 78 publications

Genome-wide SNP identification in Prunus rootstocks germplasm collections using Genotyping-by-Sequencing: phylogenetic analysis, distribution of SNPs and prediction of their effect on gene function

Genome-wide SNP identification in Prunus rootstocks germplasm collections using Genotyping-by-Sequencing: phylogenetic analysis, distribution of SNPs and prediction of their effect on gene function

High-quality chromosome-scale assembly of the walnut (Juglans regiaL) reference genome

Genome-Wide Analysis of Basic Helix-Loop-Helix (bHLH) TFs in Sea Buckthorn (Hippophae rhamnoides)

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